Sponsons won't scrub any top speed. They don't touch the water unless you are turning. BUT.... when you turn, they dig in, and help you cut harder.
NOW... and intake grate can scrub top speed. And yes... a very aggressive, "Top-Loader" type grate, in smooth water, can kill your top speed by 5mph. The falls under the heading of "Give and take" If you are racing... or riding in very choppy water... a top loader will keep they pump loaded, and in turn, keep your top speeds higher than with a standard intake.
Think of it this way... if you put an off-road tire on your truck... you would expect it to hook up well at the drag strip.... would you??
As a general rule... on a sit-down ski, being run in a lake... I don't mess with it too much. If you are running in choppy conditions most of the time... a mild top-loader with a skat-trak "Swirl" impeller will help keep you moving.
Sponsons are up to you. Unless you are racing... they will take some of the "Fun" away from the ski. (won't let you slide and spin as easy)